Raman microspectroscopy detects epigenetic modifications in living Jurkat leukemic cells

Tracking intracellular nuclear targeted-chemotherapy of chidamide-loaded Prussian blue nanocarriers by SERS mapping

The novel histone deacetylase drug chidamide (CHI) has been proven to regulate gene expression associated with oncogenesis via epigenetic mechanisms. However, huge side effects such as non-targeting, poor intracellular accumulation and low nuclear entry efficiency severely restrict its therapeutic efficacy. Dual-targeted nanodrug delivery systems have been proposed as the solution. Herein, we developed a CHI-loaded drug delivery nanosystem based on Prussian blue (PB) nanocarrier, which combines surface-enhanced Raman scattering (SERS) tracking function with cancer cell/nuclear-targeted chemotherapy capability. With the property of background-free SERS mapping, PB nanocarriers can serve as tracking agents to localize intracellular CHI. The incorporation of targeted molecules specifically enhances the cancer cell/nuclear internalization and chemotherapeutic effects of CHI-loaded PB nanocarriers. In vitro cytotoxicity assay clearly shows that the constructed CHI-loaded PB nanocarriers have significant inhibitory on Jurkat cell proliferation. Furthermore, SERS spectral analysis of Jurkat cells incubated with the CHI-loaded PB nanocarriers reveals obvious features of cellular apoptosis: DNA skeleton fragmentation, chromatin depolymerization, histone acetylation, and nucleosome conformation change. Importantly, this CHI-loaded PB nanocarrier will provide a new insight for lymphoblastic leukemia targeted chemotherapy.

In situ exploring Chidamide, a histone deacetylase inhibitor, induces molecular changes of leukemic T-lymphocyte apoptosis using Raman spectroscopy

Though it has been demonstrated that Chidamide (CS055/HBI-8000), a novel benzamide class of histone deacetylase (HDAC) subtype-selectively inhibitor, reveals better anticancer effect in acute leukemia, but it remains unknown about the precise mechanism of Chidamide-induced acute leukemia cell apoptosis due to the lack of in situ molecular changes information. Based on Raman spectral analysis, we find that the action of Chidamide on Jurkat cell will lead to an addition of an acetyl group to a specific lysine residue at the end of histone amino acid, and greatly enhance the acetylation of histones H1, H2A, H2B, H3, and H4, and then destroy the electrostatic force between the alkaline terminal of the positive charged arginine side chain and the negative charged DNA of phosphate group, finally cause the depolymerization of DNA and histone octamer in chromatin nucleosome depolymerization and the relaxation of chromatin. Accordingly, the accumulation of reactive oxygen species (ROS) and the decreasing of mitochondrial membrane potential (MMP) are observed. For comparison, we also present the corresponding results of suberoylanilide hydroxamic acid (SAHA) and MS-275 inhibitors. The achieved results show that proliferation of Chidamide-treated Jurkat cells is low relative to MS-275 or SAHA, and the action of Chidamide or MS-275 on Jurkat cells lead to obvious increasing in histones H1, H2A, H2B, H3, and H4, whereas the action effect of SAHA is mainly observed in histones H1, H2A, H2B, H3 but weak in histone H4. Moreover, it is found that Chidamide-induced histone H3 acetylation in Jurkat cells is stronger than MS-275 and SAHA. Collectively, by Raman spectral analysis, we achieve the dynamic behavior of biochemical components, molecular conformation and morphological changes of HDAC inhibitors-treated Jurkat cells. Importantly, our research is the first to demonstrate that the action site of HDAC inhibitors on Jurkat cell is located in the DNA minor groove. Most importantly, the application of Raman spectrum in exploring in-situ molecular changes information, histone acetylation modification in epigenetics, drug action sites and cell cycle affected by HDAC inhibitors will supply new idea and reference for the design and modification of HDAC inhibitors.

Monitoring the molecular composition of live cells exposed to electric pulses via label-free optical methods

The permeabilization of the live cells membrane by the delivery of electric pulses has fundamental interest in medicine, in particular in tumors treatment by electrochemotherapy. Since underlying mechanisms are still not fully understood, we studied the impact of electric pulses on the biochemical composition of live cells thanks to label-free optical methods: confocal Raman microspectroscopy and terahertz microscopy. A dose effect was observed after cells exposure to different field intensities and a major impact on cell peptide/protein content was found. Raman measurements reveal that protein structure and/or environment are modified by the electric pulses while terahertz measurements suggest a leakage of proteins and other intracellular compounds. We show that Raman and terahertz modalities are a particularly attractive complement to fluorescence microscopy which is the reference optical technique in the case of electropermeabilization. Finally, we propose an analytical model for the influx and efflux of non-permeant molecules through transiently (electro)permeabilized cell membranes.

Implementation of a classification strategy of Raman data collected in different clinical conditions: application to the diagnosis of chronic lymphocytic leukemia

The literature is rich in proof of concept studies demonstrating the potential of Raman spectroscopy for disease diagnosis. However, few studies are conducted in a clinical context to demonstrate its applicability in current clinical practice and workflow. Indeed, this translational research remains far from the patient's bedside for several reasons. First, samples are often cultured cell lines. Second, they are prepared on non-standard substrates for clinical routine. Third, a unique supervised classification model is usually constructed using inadequate cross-validation strategy. Finally, the implemented models maximize classification accuracy without taking into account the clinician's needs. In this paper, we address these issues through a diagnosis problem in real clinical conditions, i.e., the diagnosis of chronic lymphocytic leukemia from fresh unstained blood smears spread on glass slides. From Raman data acquired in different experimental conditions, a repeated double cross-validation strategy was combined with different cross-validation approaches, a consensus label strategy and adaptive thresholds able to adapt to the clinician's needs. Combined with validation at the patient level, classification results were improved compared to traditional strategies.

In vivo detection of drug-induced apoptosis in tumors using Raman spectroscopy

We describe a label-free approach based on Raman spectroscopy, to study drug-induced apoptosis in vivo. Spectral-shifts at wavenumbers associated with DNA, proteins, lipids, and collagen have been identified on breast and melanoma tumor tissues. These findings may enable a new analytical method for rapid readout of drug-therapy with miniaturized probes.

Non-Invasive Approaches to Epigenetic-Based Sperm Selection

Since sperm size and form do not necessarily provide information on internal sperm structures, novel sperm markers need to be found in order to conduct assisted reproductive therapies (ART) successfully. Currently, the priority of andrologists is not only to select those sperm able to fertilize the oocyte, but also a high quality of sperm that will guarantee a healthy embryo. Evidence of this shows us the importance of studying sperm intensively on genetic and epigenetic levels, because these could probably be the cause of a percentage of infertility diagnosed as idiopathic. Thus, more attention is being paid to posttranslational modifications as the key for better understanding of the fertilization process and its impact on embryo and offspring. Advances in the discovery of new sperm markers should go hand in hand with finding appropriate techniques for selecting the healthiest sperm, guaranteeing its non-invasiveness. To date, most sperm selection techniques can be harmful to sperm due to centrifugation or staining procedures. Some methods, such as microfluidic techniques, sperm nanopurifications, and Raman spectroscopy, have the potential to make selection gentle to sperm, tracking small abnormalities undetected by methods currently used. The fact that live cells could be analyzed without harmful effects creates the expectation of using them routinely in ART. In this review, we focus on the combination of sperm epigenetic status (modifications) as quality markers, with non-invasive sperm selection methods as novel approaches to improve ART outcomes.

The Feulgen reaction: A brief review and new perspectives

The Feulgen reaction has been proposed by Robert Feulgen and Heinrich Rossenbeck for the identification of DNA nearly a hundred years ago. Since then, many other applications of this cytochemical/topochemical procedure at qualitative and quantitative level have been proposed in relation to DNA and its role in chromatin in human, animal and plant cells. In this article, we briefly review some fundamental aspects of the Feulgen reaction and current applications of such a method in studies of altered chromatin texture, including its association with or preceding changes in transcriptional activities and effect on epigenetic marks. Further perspectives on the use of the Feulgen reaction will depend of the proposal of innovative biological questions in which its reveals appropriate.

Demonstration of the Protein Involvement in Cell Electropermeabilization using Confocal Raman Microspectroscopy

Confocal Raman microspectroscopy was used to study the interaction between pulsed electric fields and live cells from a molecular point of view in a non-invasive and label-free manner. Raman signatures of live human adipose-derived mesenchymal stem cells exposed or not to pulsed electric fields (8 pulses, 1 000 V/cm, 100 μs, 1 Hz) were acquired at two cellular locations (nucleus and cytoplasm) and two spectral bands (600–1 800 cm⁻¹ and 2 800–3 100 cm⁻¹). Vibrational modes of proteins (phenylalanine and amide I) and lipids were found to be modified by the electropermeabilization process with a statistically significant difference. The relative magnitude of four phenylalanine peaks decreased in the spectra of the pulsed group. On the contrary, the relative magnitude of the amide I band at 1658 cm⁻¹ increased by 40% when comparing pulsed and control group. No difference was found between the control and the pulsed group in the high wavenumber spectral band. Our results reveal the modification of proteins in living cells exposed to pulsed electric fields by means of confocal Raman microspectroscopy.

Diagnosis approach of chronic lymphocytic leukemia on unstained blood smears using Raman microspectroscopy and supervised classification

We have investigated the potential of Raman microspectroscopy combined with supervised classification algorithms to diagnose a blood lymphoproliferative disease, namely chronic lymphocytic leukemia (CLL). This study was conducted directly on human blood smears (27 volunteers and 49 CLL patients) spread on standard glass slides according to a cytological protocol before the staining step. Visible excitation at 532 nm was chosen, instead of near infrared, in order to minimize the glass contribution in the Raman spectra. After Raman measurements, blood smears were stained using the May-Grünwald Giemsa procedure to correlate spectroscopic data classifications with cytological analysis. A first prediction model was built using support vector machines to discriminate between the two main leukocyte subpopulations (lymphocytes and polymorphonuclears) with sensitivity and specificity over 98.5%. The spectral differences between these two classes were associated to higher nucleic acid content in lymphocytes compared to polymorphonuclears. Then, we developed a classification model to discriminate between neoplastic and healthy lymphocyte spectra, with a mean sensitivity and specificity of 88% and 91% respectively. The main molecular differences between healthy and CLL cells were associated with DNA and protein changes. These spectroscopic markers could lead, in the future, to the development of a helpful medical tool for CLL diagnosis.

Cellular Cholesterol Distribution Influences Proteolytic Release of the LRP-1 Ectodomain

Low-density lipoprotein receptor-related protein-1 (LRP-1) is a multifunctional matricellular receptor composed of a large ligand-binding subunit (515-kDa α-chain) associated with a short trans-membrane subunit (85-kDa β-chain). LRP-1, which exhibits both endocytosis and cell signaling properties, plays a key role in tumor invasion by regulating the activity of proteinases such as matrix metalloproteinases (MMPs). LRP-1 is shed at the cell surface by proteinases such as membrane-type 1 MMP (MT1-MMP) and a disintegrin and metalloproteinase-12 (ADAM-12). Here, we show by using biophysical, biochemical, and cellular imaging approaches that efficient extraction of cell cholesterol and increased LRP-1 shedding occur in MDA-MB-231 breast cancer cells but not in MDA-MB-435 cells. Our data show that cholesterol is differently distributed in both cell lines; predominantly intracellularly for MDA-MB-231 cells and at the plasma membrane for MDA-MB-435 cells. This study highlights the relationship between the rate and cellular distribution of cholesterol and its impact on LRP-1 shedding modulation. Altogether, our data strongly suggest that the increase of LRP-1 shedding upon cholesterol depletion induces a higher accessibility of the sheddase substrate, i.e., LRP-1, at the cell surface rather than an increase of expression of the enzyme.

Visualizing the appearance and disappearance of the attractor of differentiation using Raman spectral imaging

Using Raman spectral imaging, we visualized the cell state transition during differentiation and constructed hypothetical potential landscapes for attractors of cellular states on a state space composed of parameters related to the shape of the Raman spectra. As models of differentiation, we used the myogenic C2C12 cell line and mouse embryonic stem cells. Raman spectral imaging can validate the amounts and locations of multiple cellular components that describe the cell state such as proteins, nucleic acids, and lipids; thus, it can report the state of a single cell. Herein, we visualized the cell state transition during differentiation using Raman spectral imaging of cell nuclei in combination with principal component analysis. During differentiation, cell populations with a seemingly homogeneous cell state before differentiation showed heterogeneity at the early stage of differentiation. At later differentiation stages, the cells returned to a homogeneous cell state that was different from the undifferentiated state. Thus, Raman spectral imaging enables us to illustrate the disappearance and reappearance of an attractor in a differentiation landscape, where cells stochastically fluctuate between states at the early stage of differentiation.

Automated Quantification of Tumor Viability in a Rabbit Liver Tumor Model after Chemoembolization Using Infrared Imaging

The rabbit VX2 tumor is a fast-growing carcinoma model commonly used to study new therapeutic devices, such as catheter-based therapies for patients with inoperable hepatocellular carcinoma. The evaluation of tumor viability after such locoregional therapies is essential to directing hepatocellular carcinoma management. We used infrared microspectroscopy for the automatic characterization and quantification of the VX2 liver tumor viability after drug-eluting beads transarterial chemoembolization (DEB-TACE). The protocol consisted of K-means clustering followed by principal component analysis (PCA) and linear discriminant analysis (LDA). The K-means clustering was used to classify the spectra from the infrared images of control or treated tumors and to build a database of many tissue spectra. On the basis of this reference library, the PCA-LDA analysis was used to build a predictive model to identify and quantify automatically tumor viability on unknown tissue sections. For the DEB group, the LDA model determined that the surface of tumor necrosis represented 91.6% ± 8.9% (control group: 33.1% ± 19.6%; Mann-Whitney P = 0.0004) and the viable tumor 2.6% ± 4% (control group: 62.2% ± 15.2%; Mann-Whitney P = 0.0004). Tissue quantification measurements correlated well with tumor necrosis (r = 0.827, P < 0.0001) and viable tumor (r = 0.840, P < 0.0001). Infrared imaging and PCA-LDA analysis could be helpful for easily assessing tumor viability.

Visualizing cell state transition using Raman spectroscopy

System level understanding of the cell requires detailed description of the cell state, which is often characterized by the expression levels of proteins. However, understanding the cell state requires comprehensive information of the cell, which is usually obtained from a large number of cells and their disruption. In this study, we used Raman spectroscopy, which can report changes in the cell state without introducing any label, as a non-invasive method with single cell capability. Significant differences in Raman spectra were observed at the levels of both the cytosol and nucleus in different cell-lines from mouse, indicating that Raman spectra reflect differences in the cell state. Difference in cell state was observed before and after the induction of differentiation in neuroblastoma and adipocytes, showing that Raman spectra can detect subtle changes in the cell state. Cell state transitions during embryonic stem cell (ESC) differentiation were visualized when Raman spectroscopy was coupled with principal component analysis (PCA), which showed gradual transition in the cell states during differentiation. Detailed analysis showed that the diversity between cells are large in undifferentiated ESC and in mesenchymal stem cells compared with terminally differentiated cells, implying that the cell state in stem cells stochastically fluctuates during the self-renewal process. The present study strongly indicates that Raman spectral morphology, in combination with PCA, can be used to establish cells' fingerprints, which can be useful for distinguishing and identifying different cellular states.

Epigenetically induced changes in nuclear textural patterns and gelatinase expression in human fibrosarcoma cells

OBJECTIVE

Chromatin texture patterns of tumour cell nuclei can serve as cancer biomarkers, either to define diagnostic classifications or to obtain relevant prognostic information, in a large number of human tumours. Epigenetic mechanisms, mainly DNA methylation and histone post-translational modification, have been shown to influence chromatin packing states, and therefore nuclear texture. The aim of this study was to analyse effects of these two mechanisms on chromatin texture, and also on correlation with gelatinase expression, in human fibrosarcoma tumour cells.

MATERIALS AND METHODS

We investigated effects of DNA hypomethylating agent 5-aza-2'-deoxycytidine (5-azadC) and histone deacetylase inhibitor trichostatin A (TSA) on nuclear textural characteristics of human HT1080 fibrosarcoma cells, evaluated by image cytometry, and expression of gelatinases MMP-2 and MMP-9, two metalloproteinases implicated in cancer progression and metastasis.

RESULTS

5-azadC induced significant variation in chromatin higher order organization, particularly chromatin decondensation, associated with reduction in global DNA methylation, concomitantly with increase in MMP-9, and to a lesser extent, MMP-2 expression. TSA alone did not have any effect on HT1080 cells, but exhibited differential activity when added to cells treated with 5-azadC. When treated with both drugs, nuclei had higher texture abnormalities. In this setting, reduction in MMP-9 expression was observed, whereas MMP-2 expression remained unaffected.

CONCLUSIONS

These data show that hypomethylating drug 5-azadC and histone deacetylase inhibitor TSA were able to induce modulation of higher order chromatin organization and gelatinase expression in human HT1080 fibrosarcoma cells.

Recent advances in laser tweezers Raman spectroscopy (LTRS) for label-free analysis of single cells

Laser tweezers Raman spectroscopy (LTRS), a technique that integrates optical tweezers with confocal Raman spectroscopy, is a variation of micro-Raman spectroscopy that enables the manipulation and biochemical analysis of single biological particles in suspension. This article provides an overview of the LTRS method, with an emphasis on highlighting recent advances over the past several years in the development of the technology and several new biological and biomedical applications that have been demonstrated. A perspective on the future developments of this powerful cytometric technology will also be presented.

Changes in the infrared microspectroscopic characteristics of DNA caused by cationic elements, different base richness and single-stranded form

BACKGROUND

The infrared (IR) analysis of dried samples of DNA and DNA-polypeptide complexes is still scarce. Here we have studied the FT-IR profiles of these components to further the understanding of the FT-IR signatures of chromatin and cell nuclei.

METHODOLOGY/PRINCIPAL FINDINGS

Calf thymus and salmon testis DNA, and complexes of histone H1, protamine, poly-L-lysine and poly-L-arginine (histone-mimic macromolecules) with DNA were analyzed in an IR microspectroscope equipped with an attenuated total reflection diamond objective and Grams software. Conditions including polypeptides bound to the DNA, DNA base composition, and single-stranded form were found to differently affect the vibrational characteristics of the chemical groups (especially, PO(2)(-)) in the nucleic acid. The antisymmetric stretching (ν(as)) of the DNA PO(2)(-) was greater than the symmetric stretching (ν(s)) of these groups and increased in the polypeptide-DNA complexes. A shift of the ν(as) of the DNA PO(2)(-) to a lower frequency and an increased intensity of this vibration were induced especially by lysine-rich histones. Lysine richness additionally contributed to an increase in the vibrational stretching of the amide I group. Even in simple molecules such as inorganic phosphates, the vibrational characteristics of the phosphate anions were differently affected by different cations. As a result of the optimization of the DNA conformation by binding to arginine-rich polypeptides, enhancements of the vibrational characteristics in the FT-IR fingerprint could be detected. Although different profiles were obtained for the DNA with different base compositions, this situation was no longer verified in the polypeptide-DNA complexes and most likely in isolated chromatin or cell nuclei. However, the ν(as) PO(2)(-)/ν(s) PO(2)(-) ratio could discriminate DNA with different base compositions and DNA in a single-stranded form.

CONCLUSIONS/SIGNIFICANCE

FT-IR spectral profiles are a valuable tool for establishing the vibrational characteristics of individualized chromatin components, such as DNA and DNA-polypeptide complexes in dried samples.